Articles | Volume 14, issue 11
https://doi.org/10.5194/gmd-14-7155-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-14-7155-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
OMEN-SED(-RCM) (v1.1): a pseudo-reactive continuum representation of organic matter degradation dynamics for OMEN-SED
BGeosys, Department of Geoscience, Environment & Society (DGES), Université Libre de Bruxelles, Brussels, Belgium
current address: Department of Earth Sciences, VU University of Amsterdam, 1081 HV Amsterdam, the Netherlands
Dominik Hülse
Department of Earth Sciences, University of California, Riverside, CA, USA
Sandra Arndt
BGeosys, Department of Geoscience, Environment & Society (DGES), Université Libre de Bruxelles, Brussels, Belgium
Related authors
Niek Jesse Speetjens, Gustaf Hugelius, Thomas Gumbricht, Hugues Lantuit, Wouter R. Berghuijs, Philip A. Pika, Amanda Poste, and Jorien E. Vonk
Earth Syst. Sci. Data, 15, 541–554, https://doi.org/10.5194/essd-15-541-2023, https://doi.org/10.5194/essd-15-541-2023, 2023
Short summary
Short summary
The Arctic is rapidly changing. Outside the Arctic, large databases changed how researchers look at river systems and land-to-ocean processes. We present the first integrated pan-ARctic CAtchments summary DatabasE (ARCADE) (> 40 000 river catchments draining into the Arctic Ocean). It incorporates information about the drainage area with 103 geospatial, environmental, climatic, and physiographic properties and covers small watersheds , which are especially subject to change, at a high resolution
Dirk Jong, Lisa Bröder, Tommaso Tesi, Kirsi H. Keskitalo, Nikita Zimov, Anna Davydova, Philip Pika, Negar Haghipour, Timothy I. Eglinton, and Jorien E. Vonk
Biogeosciences, 20, 271–294, https://doi.org/10.5194/bg-20-271-2023, https://doi.org/10.5194/bg-20-271-2023, 2023
Short summary
Short summary
With this study, we want to highlight the importance of studying both land and ocean together, and water and sediment together, as these systems function as a continuum, and determine how organic carbon derived from permafrost is broken down and its effect on global warming. Although on the one hand it appears that organic carbon is removed from sediments along the pathway of transport from river to ocean, it also appears to remain relatively ‘fresh’, despite this removal and its very old age.
Felipe S. Freitas, Philip A. Pika, Sabine Kasten, Bo B. Jørgensen, Jens Rassmann, Christophe Rabouille, Shaun Thomas, Henrik Sass, Richard D. Pancost, and Sandra Arndt
Biogeosciences, 18, 4651–4679, https://doi.org/10.5194/bg-18-4651-2021, https://doi.org/10.5194/bg-18-4651-2021, 2021
Short summary
Short summary
It remains challenging to fully understand what controls carbon burial in marine sediments globally. Thus, we use a model–data approach to identify patterns of organic matter reactivity at the seafloor across distinct environmental conditions. Our findings support the notion that organic matter reactivity is a dynamic ecosystem property and strongly influences biogeochemical cycling and exchange. Our results are essential to improve predictions of future changes in carbon cycling and climate.
Manon Maisonnier, Maoyuan Feng, David Bastviken, Sandra Arndt, Ronny Lauerwald, Aidin Jabbari, Goulven Gildas Laruelle, Murray D. MacKay, Zeli Tan, Wim Thiery, and Pierre Regnier
EGUsphere, https://doi.org/10.5194/egusphere-2025-1306, https://doi.org/10.5194/egusphere-2025-1306, 2025
Short summary
Short summary
A new process-based modelling framework, FLaMe v1.0 (Fluxes of Lake Methane version 1.0), is developed to simulate methane (CH4) emissions from lakes at large scales. FLaMe couples the dynamics of organic carbon, oxygen and methane in lakes and rests on an innovative, computationally efficient lake clustering approach for the simulation of CH4 emissions across a large number of lakes. The model evaluation suggests that FLaMe captures the sub-annual and spatial variability of CH4 emissions well.
Sinan Xu, Bo Liu, Sandra Arndt, Sabine Kasten, and Zijun Wu
Biogeosciences, 20, 2251–2263, https://doi.org/10.5194/bg-20-2251-2023, https://doi.org/10.5194/bg-20-2251-2023, 2023
Short summary
Short summary
We use a reactive continuum model based on a lognormal distribution (l-RCM) to inversely determine model parameters μ and σ at 123 sites across the global ocean. Our results show organic matter (OM) reactivity is more than 3 orders of magnitude higher in shelf than in abyssal regions. In addition, OM reactivity is higher than predicted in some specific regions, yet the l-RCM can still capture OM reactivity features in these regions.
Niek Jesse Speetjens, Gustaf Hugelius, Thomas Gumbricht, Hugues Lantuit, Wouter R. Berghuijs, Philip A. Pika, Amanda Poste, and Jorien E. Vonk
Earth Syst. Sci. Data, 15, 541–554, https://doi.org/10.5194/essd-15-541-2023, https://doi.org/10.5194/essd-15-541-2023, 2023
Short summary
Short summary
The Arctic is rapidly changing. Outside the Arctic, large databases changed how researchers look at river systems and land-to-ocean processes. We present the first integrated pan-ARctic CAtchments summary DatabasE (ARCADE) (> 40 000 river catchments draining into the Arctic Ocean). It incorporates information about the drainage area with 103 geospatial, environmental, climatic, and physiographic properties and covers small watersheds , which are especially subject to change, at a high resolution
Dirk Jong, Lisa Bröder, Tommaso Tesi, Kirsi H. Keskitalo, Nikita Zimov, Anna Davydova, Philip Pika, Negar Haghipour, Timothy I. Eglinton, and Jorien E. Vonk
Biogeosciences, 20, 271–294, https://doi.org/10.5194/bg-20-271-2023, https://doi.org/10.5194/bg-20-271-2023, 2023
Short summary
Short summary
With this study, we want to highlight the importance of studying both land and ocean together, and water and sediment together, as these systems function as a continuum, and determine how organic carbon derived from permafrost is broken down and its effect on global warming. Although on the one hand it appears that organic carbon is removed from sediments along the pathway of transport from river to ocean, it also appears to remain relatively ‘fresh’, despite this removal and its very old age.
James P. J. Ward, Katharine R. Hendry, Sandra Arndt, Johan C. Faust, Felipe S. Freitas, Sian F. Henley, Jeffrey W. Krause, Christian März, Allyson C. Tessin, and Ruth L. Airs
Biogeosciences, 19, 3445–3467, https://doi.org/10.5194/bg-19-3445-2022, https://doi.org/10.5194/bg-19-3445-2022, 2022
Short summary
Short summary
The seafloor plays an important role in the cycling of silicon (Si), a key nutrient that promotes marine primary productivity. In our model study, we disentangle major controls on the seafloor Si cycle to better anticipate the impacts of continued warming and sea ice melt in the Barents Sea. We uncover a coupling of the iron redox and Si cycles, dissolution of lithogenic silicates, and authigenic clay formation, comprising a Si sink that could have implications for the Arctic Ocean Si budget.
Yoshiki Kanzaki, Dominik Hülse, Sandra Kirtland Turner, and Andy Ridgwell
Geosci. Model Dev., 14, 5999–6023, https://doi.org/10.5194/gmd-14-5999-2021, https://doi.org/10.5194/gmd-14-5999-2021, 2021
Short summary
Short summary
Sedimentary carbonate plays a central role in regulating Earth’s carbon cycle and climate, and also serves as an archive of paleoenvironments, hosting various trace elements/isotopes. To help obtain
trueenvironmental changes from carbonate records over diagenetic distortion, IMP has been newly developed and has the capability to simulate the diagenesis of multiple carbonate particles and implement different styles of particle mixing by benthos using an adapted transition matrix method.
Felipe S. Freitas, Philip A. Pika, Sabine Kasten, Bo B. Jørgensen, Jens Rassmann, Christophe Rabouille, Shaun Thomas, Henrik Sass, Richard D. Pancost, and Sandra Arndt
Biogeosciences, 18, 4651–4679, https://doi.org/10.5194/bg-18-4651-2021, https://doi.org/10.5194/bg-18-4651-2021, 2021
Short summary
Short summary
It remains challenging to fully understand what controls carbon burial in marine sediments globally. Thus, we use a model–data approach to identify patterns of organic matter reactivity at the seafloor across distinct environmental conditions. Our findings support the notion that organic matter reactivity is a dynamic ecosystem property and strongly influences biogeochemical cycling and exchange. Our results are essential to improve predictions of future changes in carbon cycling and climate.
Sebastiaan J. van de Velde, Dominik Hülse, Christopher T. Reinhard, and Andy Ridgwell
Geosci. Model Dev., 14, 2713–2745, https://doi.org/10.5194/gmd-14-2713-2021, https://doi.org/10.5194/gmd-14-2713-2021, 2021
Short summary
Short summary
Biogeochemical interactions between iron and sulfur are central to the long-term biogeochemical evolution of Earth’s oceans. Here, we introduce an iron–sulphur cycle in a model of Earth's oceans. Our analyses show that the results of the model are robust towards parameter choices and that simulated concentrations and reactions are comparable to those observed in ancient ocean analogues (anoxic lakes). Our model represents an important step forward in the study of iron–sulfur cycling.
Cited articles
Aguilera, D. R., Jourabchi, P., Spiteri, C., and Regnier, P.: A
knowledge-based reactive transport approach for the simulation of
biogeochemical dynamics in Earth systems, Geochem. Geophy.
Geosy., 6, 1–18, https://doi.org/10.1029/2004GC000899, 2005. a
Aller, R.: 8.11 – Sedimentary Diagenesis, Depositional Environments, and
Benthic Fluxes, in: Treatise on Geochemistry (Second Edition), edited by:
Holland, H. D. and Turekian, K. K., Elsevier, Oxford, 2nd
Edn., 8, 293–334, https://doi.org/10.1016/B978-0-08-095975-7.00611-2, 2014. a
Aller, R. C. and Blair, N. E.: Carbon remineralization in the Amazon-Guianas
tropical mobile mudbelt: A sedimentary incinerator, Cont. Shelf
Res., 26, 2241–2259, https://doi.org/10.1016/j.csr.2006.07.016, 2006. a
Archer, D. and Maier-Reimer, E.: Effect of deep-sea sedimentary calcite
preservation on atmospheric CO2 concentration, Nature, 367, 260–263,
https://doi.org/10.1038/367260a0, 1994. a
Aris, R.: Prolegomena to the rational analysis of systems of chemical reactions
II. Some addenda, Arch. Ration. Mech. An., 27, 356–364,
1968. a
Arndt, S., Jørgensen, B. B., LaRowe, D. E., Middelburg, J. J., Pancost,
R. D., and Regnier, P.: Quantifying the degradation of organic matter in
marine sediments: A review and synthesis, Earth-Sci. Rev., 123,
53–86, https://doi.org/10.1016/j.earscirev.2013.02.008, 2013. a, b, c, d, e, f, g, h, i, j, k, l, m, n
Berner, R. A.: A model for atmospheric CO2 over Phanerozoic time, Am.
J. Sci., 291, 339–376, https://doi.org/10.2475/ajs.291.4.339, 1991. a
Billen, G.: An idealized model of nitrogen recycling in marine sediments,
Am. J. Sci., 282, 512–541, 1982. a
Black, K. S., Fones, G. R., Peppe, O. C., Kennedy, H. A., and Bentaleb, I.: An
autonomous benthic lander:, Cont. Shelf Res., 21, 859–877,
https://doi.org/10.1016/S0278-4343(00)00116-3, 2001. a
Bohlen, L., Dale, A. W., and Wallmann, K.: Simple transfer functions for
calculating benthic fixed nitrogen losses and C : N : P regeneration ratios
in global biogeochemical models, Global Biogeochem. Cy., 26, GB3029,
https://doi.org/10.1029/2011GB004198, 2012. a
Boudreau, B. P.: A method-of-lines code for carbon and nutrient diagenesis in
aquatic sediments, Comput. Geosci., 22, 479–496,
https://doi.org/10.1016/0098-3004(95)00115-8, 1996. a
Boudreau, B. P.: Mean mixed depth of sediments: The wherefore and the why,
Limnol. Oceanogr., 43, 524–526, https://doi.org/10.4319/lo.1998.43.3.0524,
1998. a
Boudreau, B. P. and Arnosti, C.: Comment on “Physical Model for the Decay and
Preservation of Marine Organic Carbon”, Science, 319, 1616–1616,
https://doi.org/10.1126/science.1148589, 2008. a
Boyer, T. P., Antonov, J. I., Baranova, O. K., Garcia, H. E., Johnson, D. R.,
Locarnini, R. A., Mishonov, A. V., O'Brien, T. O., Seidov, D., Smolyar,
I. V., and Zweng, M. M.: World Ocean Database 2009, in: NOAA Atlas NESDIS
66, p. 216, https://doi.org/10.1029/2009EO490003, 2009. a
Burwicz, E., Rüpke, L., and Wallmann, K.: Estimation of the global
amount of submarine gas hydrates formed via microbial methane formation based
on numerical reaction-transport modeling and a novel parameterization of
Holocene sedimentation, Geochim. Cosmochim. Ac., 75, 4562–4576,
https://doi.org/10.1016/j.gca.2011.05.029, 2011. a
Canfield, D., Jørgensen, B., Fossing, H., Glud, R., Gundersen, J., Ramsing,
N., Thamdrup, B., Hansen, J., Nielsen, L., and Hall, P.: Pathways of organic
carbon oxidation in three continental margin sediments, Mar. Geol., 113,
27–40, https://doi.org/10.1016/0025-3227(93)90147-N, 1993. a
Conkright, M. E., Locarnini, R. A., Garcia, H. E., O'Brien, T. D., Boyer,
T. P., Stephens, C., and Antonov, J. I.: World Ocean Atlas 2001: Objective
analyses, data statistics, and figures: CD-ROM documentation, US Department
of Commerce, National Oceanic and Atmospheric Administration, National
Oceanographic Data Center, Ocean Climate Laboratory, National Oceanographic Data Center, Silver Spring, MD, 2002. a
Dale, A. W., Nickelsen, L., Scholz, F., Hensen, C., Oschlies, A., and Wallmann,
K.: A revised global estimate of dissolved iron fluxes from marine
sediments, Global Biogeochem. Cy., 29, 691–707,
https://doi.org/10.1002/2014GB005017, 2015. a
D'Hondt, S., Inagaki, F., Zarikian, C. A., Abrams, L. J., Dubois, N.,
Engelhardt, T., Evans, H., Ferdelman, T., Gribsholt, B., Harris, R. N.,
Hoppie, B. W., Hyun, J.-H., Kallmeyer, J., Kim, J., Lynch, J. E., McKinley,
C. C., Mitsunobu, S., Morono, Y., Murray, R. W., Pockalny, R., Sauvage, J.,
Shimono, T., Shiraishi, F., Smith, D. C., Smith-Duque, C. E., Spivack, A. J.,
Steinsbu, B. O., Suzuki, Y., Szpak, M., Toffin, L., Uramoto, G., Yamaguchi,
Y. T., Zhang, G.-l., Zhang, X.-H., and Ziebis, W.: Presence of oxygen and
aerobic communities from sea floor to basement in deep-sea sediments, Nat.
Geosci., 8, 299–304, https://doi.org/10.1038/ngeo2387, 2015. a, b, c
Egger, M., Riedinger, N., Mogollón, J. M., and Jørgensen, B. B.:
Global diffusive fluxes of methane in marine sediments, Nat. Geosci.,
11, 421–425, https://doi.org/10.1038/s41561-018-0122-8, 2018. a, b, c, d
Forney, D. C. and Rothman, D. H.: Inverse method for estimating respiration
rates from decay time series, Biogeosciences, 9, 3601–3612,
https://doi.org/10.5194/bg-9-3601-2012, 2012. a
Freitas, F. S., Pika, P. A., Kasten, S., Jørgensen, B. B., Rassmann, J., Rabouille, C., Thomas, S., Sass, H., Pancost, R. D., and Arndt, S.: New insights into large-scale trends of apparent organic matter reactivity in marine sediments and patterns of benthic carbon transformation, Biogeosciences, 18, 4651–4679, https://doi.org/10.5194/bg-18-4651-2021, 2021. a, b, c, d, e
Giordani, P., Helder, W., Koning, E., Miserocchi, S., Danovaro, R., and
Malaguti, A.: Gradients of benthic-pelagic coupling and carbon budgets in
the Adriatic and Northern Ionian Sea, J. Mar. Syst., 33–34,
365–387, https://doi.org/10.1016/S0924-7963(02)00067-2, 2002. a
Glud, R., Gundersen, J. K., Barker Jørgensen, B., Revsbech, N. P., and
Schulz, H. D.: Diffusive and total oxygen uptake of deep-sea sediments in
the eastern South Atlantic Ocean: in situ and laboratory measurements, Deep-Sea Res. Pt. I, 41, 1767–1788,
https://doi.org/10.1016/0967-0637(94)90072-8, 1994. a
Glud, R., Holby, O., Hoffmann, F., and Canfield, D.: Benthic mineralization
and exchange in Arctic sediments (Svalbard, Norway), Mar. Ecol. Prog.
Ser., 173, 237–251, https://doi.org/10.3354/meps173237, 1998. a
Glud, R., Gundersen, J., and Holby, O.: Benthic in situ respiration in the
upwelling area off central Chile, Mar. Ecol. Prog. Ser., 186,
9–18, https://doi.org/10.3354/meps186009, 1999. a
Glud, R. N.: Oxygen dynamics of marine sediments, Mar. Biol. Res., 4,
243–289, https://doi.org/10.1080/17451000801888726, 2008. a
Glud, R. N., Gundersen, J. K., Røy, H., and Jørgensen, B. B.: Seasonal
dynamics of benthic O2 uptake in a semienclosed bay: Importance of
diffusion and faunal activity, Limnol. Oceanogr., 48, 1265–1276,
https://doi.org/10.4319/lo.2003.48.3.1265, 2003. a
Glud, R. N., Stahl, H., Berg, P., Wenzhöfer, F., Oguri, K., and Kitazato,
H.: In situ microscale variation in distribution and consumption of 2 : A
case study from a deep ocean margin sediment (Sagami Bay, Japan), Limnol. Oceanogr., 54, 1–12, https://doi.org/10.4319/lo.2009.54.1.0001, 2009. a
Gypens, N., Lancelot, C., and Soetaert, K.: Simple parameterisations for
describing N and P diagenetic processes: Application in the North
Sea, Prog. Oceanogr., 76, 89–110,
https://doi.org/10.1016/j.pocean.2007.10.003, 2008. a
Ho, T. C. and Aris, R.: On apparent second-order kinetics, AIChE J., 33,
1050–1051, https://doi.org/10.1002/aic.690330621, 1987. a
Hülse, D. and Pika, P.: OMEN-SED: OMEN-SED with RCM approximation, Zenodo [code], https://doi.org/10.5281/zenodo.4029488, 2021. a
Hülse, D., Arndt, S., Wilson, J. D., Munhoven, G., and Ridgwell, A.:
Understanding the causes and consequences of past marine carbon cycling
variability through models, Earth-Sci. Rev., 171, 349–382,
https://doi.org/10.1016/j.earscirev.2017.06.004, 2017. a
Hülse, D., Arndt, S., Wilson, J. D., Munhoven, G., and Ridgwell, A.:
Understanding the causes and consequences of past marine carbon cycling
variability through models, Earth-Sci. Rev., 171, 349–382,
https://doi.org/10.1016/j.earscirev.2017.06.004, 2017. a
Hülse, D., Arndt, S., Daines, S., Regnier, P., and Ridgwell, A.:
OMEN-SED 1.0: a novel, numerically efficient organic matter sediment
diagenesis module for coupling to Earth system models, Geosci. Model
Dev., 11, 2649–2689, https://doi.org/10.5194/gmd-11-2649-2018, 2018. a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, aa, ab, ac, ad, ae, af, ag, ah, ai
Jahnke, R., Emerson, S., Reimers, C., Schuffert, J., Ruttenberg, K., and
Archer, D.: Benthic recycling of biogenic debris in the eastern tropical
Atlantic Ocean, Geochim. Cosmochim. Ac., 53, 2947–2960,
https://doi.org/10.1016/0016-7037(89)90171-3, 1989. a
Jørgensen, B. B.: A comparison of methods for the quantification of
bacterial sulfate reduction in coastal marine sediments: II Calculation
from mathematical models, Geomicrobiol. J., 1, 29–47,
https://doi.org/10.1080/01490457809377722, 1978. a, b, c, d
Jørgensen, B. B.: Mineralization of organic matter in the sea bed—the
role of sulphate reduction, Nature, 296, 643–645, https://doi.org/10.1038/296643a0,
1982. a
Jørgensen, B. B. and Kasten, S.: Sulfur Cycling and Methane Oxidation,
in: Marine Geochemistry, edited by: Schulz, P. D. H. D. and Zabel, D. M.,
Springer Berlin Heidelberg, 271–309,
http://link.springer.com/chapter/10.1007/3-540-32144-6_8,
2006. a
Katsev, S. and Crowe, S. A.: Organic carbon burial efficiencies in sediments:
The power law of mineralization revisited, Geology, 43, 607–610,
https://doi.org/10.1130/G36626.1, 2015. a
Lansard, B., Rabouille, C., Denis, L., and Grenz, C.: In situ oxygen uptake
rates by coastal sediments under the influence of the Rhône River (NW
Mediterranean Sea), Cont. Shelf Res., 28, 1501–1510,
https://doi.org/10.1016/j.csr.2007.10.010, 2008. a
Lansard, B., Rabouille, C., Denis, L., and Grenz, C.: Benthic remineralization
at the land-ocean interface: A case study of the Rhône River (NW
Mediterranean Sea), Estuar. Coast. Shelf Sci., 81, 544–554,
https://doi.org/10.1016/j.ecss.2008.11.025, 2009. a
LaRowe, D., Arndt, S., Bradley, J. A., Burwicz, E., Dale, A., and Amend, J.:
Organic carbon and microbial activity in marine sediments on a global scale
throughout the Quaternary, EarthArXiv, https://doi.org/10.1016/j.gca.2020.07.017, 2020a. a
LaRowe, D. E., Arndt, S., Bradley, J. A., Estes, E. R., Hoarfrost, A., Lang,
S. Q., Lloyd, K. G., Mahmoudi, N., Orsi, W. D., Shah Walter, S. R., Steen,
A. D., and Zhao, R.: The fate of organic carbon in marine sediments – New
insights from recent data and analysis, Earth-Sci. Rev., 204,
103146, https://doi.org/10.1016/j.earscirev.2020.103146, 2020b. a, b, c
Li, Y.-H. and Gregory, S.: Diffusion of ions in sea water and in deep-sea
sediments, Geochim. Cosmochim. Ac., 38, 703–714,
https://doi.org/10.1016/0016-7037(74)90145-8, 1974. a
Manzoni, S., Katul, G. G., and Porporato, A.: Analysis of soil carbon transit
times and age distributions using network theories, J. Geophys.
Res.-Biogeo., 114, G04025, https://doi.org/10.1029/2009JG001070,
2009. a
Meister, P., Liu, B., Ferdelman, T. G., Jørgensen, B. B., and Khalili, A.:
Control of sulphate and methane distributions in marine sediments by organic
matter reactivity, Geochim. Cosmochim. Ac., 104, 183–193,
https://doi.org/10.1016/j.gca.2012.11.011, 2013. a, b, c, d
Middelburg, J. J. and Meysman, F. J. R.: Burial at Sea, Science, 316,
1294–1295, https://doi.org/10.1126/science.1144001, 2007. a
Middelburg, J. J., Vlug, T., Jaco, F., and van der Nat, W. A.: Organic matter
mineralization in marine systems, Glob. Planet. Change, 8, 47–58,
https://doi.org/10.1016/0921-8181(93)90062-S, 1993. a, b
Middelburg, J. J., Soetaert, K., Herman, P. M. J., and Heip, C. H. R.:
Denitrification in marine sediments: A model study, Global Biogeochem.
Cy., 10, 661–673, https://doi.org/10.1029/96GB02562, 1996. a, b
Mostovaya, A., Hawkes, J. A., Koehler, B., Dittmar, T., and Tranvik, L. J.:
Emergence of the Reactivity Continuum of Organic Matter from Kinetics of a
Multitude of Individual Molecular Constituents, Environ. Sci.
Technol., 51, 11571–11579, https://doi.org/10.1021/acs.est.7b02876, 2017. a
Murray, J. W. and Grunmandis, V.: Oxygen Consumption in Pelagic Marine
Sediments, Science, 209, 1527–1530, https://doi.org/10.1126/science.209.4464.1527,
1980. a
Pika, P. and Hülse, D.: PhilipPika/OMEN-SED-RCM-v1.1: Including Plot Functions, Zenodo [code],
https://doi.org/10.5281/zenodo.4421777, 2021. a, b
Regnier, P., Dale, A., Arndt, S., LaRowe, D., Mogollón, J., and Van
Cappellen, P.: Quantitative analysis of anaerobic oxidation of methane
(AOM) in marine sediments: A modeling perspective, Earth-Sci. Rev.,
106, 105–130, https://doi.org/10.1016/j.earscirev.2011.01.002, 2011. a, b, c, d
Reimers, C. E., Ruttenberg, K. C., Canfield, D. E., Christiansen, M. B., and
Martin, J. B.: Porewater pH and authigenic phases formed in the uppermost
sediments of the Santa Barbara Basin, Geochim. Cosmoch. Ac.,
60, 4037–4057, https://doi.org/10.1016/S0016-7037(96)00231-1, 1996. a, b, c
Ridgwell, A. and Zeebe, R. E.: The role of the global carbonate cycle in the
regulation and evolution of the Earth system, Earth Planet. Sc.
Lett., 234, 299–315, https://doi.org/10.1016/j.epsl.2005.03.006, 2005. a
Rothman, D. H. and Forney, D. C.: Physical Model for the Decay and
Preservation of Marine Organic Carbon, Science, 316, 1325–1328,
https://doi.org/10.1126/science.1138211, 2007. a
Røy, H., Kallmeyer, J., Adhikari, R. R., Pockalny, R., Jørgensen, B. B.,
and D'Hondt, S.: Aerobic microbial respiration in 86-million-year-old
deep-sea red clay, Science, 336, 922–925, https://doi.org/10.1126/science.1219424,
2012. a, b
Ruardij, P. and Van Raaphorst, W.: Benthic nutrient regeneration in the ERSEM
ecosystem model of the North Sea, Neth. J. Sea Res., 33,
453–483, https://doi.org/10.1016/0077-7579(95)90057-8, 1995. a
Sachs, O., Sauter, E. J., Schlüter, M., Rutgers van der Loeff, M. M.,
Jerosch, K., and Holby, O.: Benthic organic carbon flux and oxygen
penetration reflect different plankton provinces in the Southern Ocean, Deep-Sea Res. Pt. I, 56, 1319–1335,
https://doi.org/10.1016/j.dsr.2009.02.003, 2009. a
Schulz, H. D.: Quantification of Early Diagenesis: Dissolved
Constituents in Pore Water and Signals in the Solid Phase, in:
Marine Geochemistry, edited by: Schulz, P. D. H. D. and Zabel, D. M.,
Springer Berlin Heidelberg, 73–124,
http://link.springer.com/chapter/10.1007/3-540-32144-6_3 (last access: 11 November 2021),
2006. a, b
Seiter, K., Hensen, C., Schröter, J., and Zabel, M.: Organic carbon
content in surface sediments – Defining regional provinces, Deep-Sea
Res. Pt. I, 51, 2001–2026,
https://doi.org/10.1016/j.dsr.2004.06.014, 2004. a, b
Seiter, K., Hensen, C., and Zabel, M.: Benthic carbon mineralization on a
global scale, Global Biogeochem. Cy., 19, 1–26,
https://doi.org/10.1029/2004GB002225, 2005. a, b
Slomp, C., Malschaert, J., and Van Raaphorst, W.: The role of adsorption in
sediment-water exchange of phosphate in North Sea continental margin
sediments, Limnol. Oceanogr., 43, 832–846, 1998. a
Slomp, C. P., Epping, E. H., Helder, W., and Van Raaphorst, W.: A key role
for iron-bound phosphorus in authigenic apatite formation in North Atlantic
continental platform sediments, J. Mar. Res., 54, 1179–1205,
https://doi.org/10.1357/0022240963213745, 1996. a
Soetaert, K., Middelburg, J. J., Herman, P. M., and Buis, K.: On the coupling
of benthic and pelagic biogeochemical models, Earth Sci. Rev., 51,
173–201, https://doi.org/10.1016/S0012-8252(00)00004-0, 2000. a
Tarutis, W. J.: On the equivalence of the power and reactive continuum models
of organic matter diagenesis, Geochim. Cosmochim. Ac., 57,
1349–1350, https://doi.org/10.1016/0016-7037(93)90071-4, 1993. a
Teal, L., Bulling, M., Parker, E., and Solan, M.: Global patterns of
bioturbation intensity and mixed depth of marine soft sediments, Aquat.c
Biol., 2, 207–218, https://doi.org/10.3354/ab00052, 2010. a
Vähätalo, A. V., Aarnos, H., and Mäntyniemi, S.:
Biodegradability continuum and biodegradation kinetics of natural organic
matter described by the beta distribution, Biogeochemistry, 100, 227–240,
https://doi.org/10.1007/s10533-010-9419-4, 2010. a, b
Van Cappellen, P. and Wang, Y.: Metal cycling in surface sediments: modeling
the interplay of transport and reaction, Metal Contaminated Aquatic
Sediments, 1st Edn., 21–64, 1995. a
Wang, Y. F. and Van Cappellen, P.: A multicomponent reactive transport model
of early diagenesis: Application to redox cycling in coastal marine
sediments, Geochim. Cosmochim. Ac., 60, 2993–3014,
https://doi.org/10.1016/0016-7037(96)00140-8, 1996. a
Wenzhöfer, F. and Glud, R. N.: Benthic carbon mineralization in the
Atlantic: A synthesis based on in situ data from the last decade, Deep-Sea
Res. Pt. I, 49, 1255–1279,
https://doi.org/10.1016/S0967-0637(02)00025-0, 2002.
a
Wenzhöfer, F., Adler, M., Kohls, O., Hensen, C., Strotmann, B., Boehme,
S., and Schulz, H.: Calcite dissolution driven by benthic mineralization in
the deep-sea: In situ measurements of Ca , pH, pCO2 and O2, Geochim.
Cosmochim. Ac., 65, 2677–2690, https://doi.org/10.1016/S0016-7037(01)00620-2,
2001a. a
Wenzhöfer, F., Holby, O., and Kohls, O.: Deep penetrating benthic oxygen
profiles measured in situ by oxygen optodes, Deep-Sea Res. Pt. I, 48, 1741–1755, https://doi.org/10.1016/S0967-0637(00)00108-4,
2001b. a
Witte, U., Aberle, N., Sand, M., and Wenzhöfer, F.: Rapid response of a
deep-sea benthic community to POM enrichment: an in situ experimental study,
Mar. Ecol. Prog. Ser., 251, 27–36, https://doi.org/10.3354/meps251027,
2003a. a
Witte, U., Wenzhöfer, F., Sommer, S., Boetius, A., Heinz, P., Aberle, N.,
Sand, M., Cremer, A., Abraham, W. R., Jørgensen, B. B., and Pfannkuche,
O.: In situ experimental evidence of the fate of a phytodetritus pulse at
the abyssal sea floor, Nature, 424, 763–766, https://doi.org/10.1038/nature01799,
2003b. a
Short summary
OMEN-SED is a model for early diagenesis in marine sediments simulating organic matter (OM) degradation and nutrient dynamics. We replaced the original description with a more realistic one accounting for the widely observed decrease in OM reactivity. The new model reproduces pore water profiles and sediment–water interface fluxes across different environments. This functionality extends the model’s applicability to a broad range of environments and timescales while requiring fewer parameters.
OMEN-SED is a model for early diagenesis in marine sediments simulating organic matter (OM)...